Hi Marcos,

Yes, I compiled with clang instead of icc (no particular reason for this; I tend to use gcc/clang). I use mpich4.1.1, which I first built with clang and ifort: 

FC=ifort

./configure --prefix=/usr/local/mpich4 --enable-two-level-namespace


Samar

On May 15, 2023, at 6:07 PM, Vanella, Marcos (Fed) <marcos.vanella@nist.gov> wrote:

Hi Samar, what MPI library do you use? Did you compile it with clang instead of icc?
Thanks,
Marcos
From: Samar Khatiwala <samar.khatiwala@earth.ox.ac.uk>
Sent: Monday, May 15, 2023 1:05 PM
To: Matthew Knepley <knepley@gmail.com>
Cc: Vanella, Marcos (Fed) <marcos.vanella@nist.gov>; petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov>
Subject: Re: [petsc-users] Compiling PETSC with Intel OneAPI compilers and OpenMPI
 
Hi, for what it’s worth, clang + ifort from OneAPI 2023 update 1 works fine for me on both Intel and M2 Macs. So it might just be a matter of upgrading. 

Samar

On May 15, 2023, at 5:53 PM, Matthew Knepley <knepley@gmail.com> wrote:

Send us

  $PETSC_ARCH/include/petscconf.h

  Thanks,

     Matt

On Mon, May 15, 2023 at 12:49 PM Vanella, Marcos (Fed) <marcos.vanella@nist.gov> wrote:
Hi Matt, I configured the lib like this:

$ ./configure --with-blaslapack-dir=/opt/intel/oneapi/mkl/2022.2.1 --with-debugging=0 --with-shared-libraries=0 --download-make

and compiled. I still get some check segfault error. See below:

$ make PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 PETSC_ARCH=arch-darwin-c-opt check
Running check examples to verify correct installation
Using PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 and PETSC_ARCH=arch-darwin-c-opt
*******************Error detected during compile or link!*******************
/Users/mnv/Documents/Software/petsc-3.19.1/src/snes/tutorials ex19
*********************************************************************************
mpicc -Wl,-bind_at_load -Wl,-multiply_defined,suppress -Wl,-multiply_defined -Wl,suppress -Wl,-commons,use_dylibs -Wl,-search_paths_first -Wl,-no_compact_unwind  -fPIC -wd1572 -Wno-unknown-pragmas -g -O3  -I/Users/mnv/Documents/Software/petsc-3.19.1/include -I/Users/mnv/Documents/Software/petsc-3.19.1/arch-darwin-c-opt/include -I/opt/X11/include  -std=c99    ex19.c  -L/Users/mnv/Documents/Software/petsc-3.19.1/arch-darwin-c-opt/lib -Wl,-rpath,/opt/intel/oneapi/mkl/2022.2.1/lib -L/opt/intel/oneapi/mkl/2022.2.1/lib -Wl,-rpath,/opt/X11/lib -L/opt/X11/lib -L/opt/openmpi414_oneapi22u3/lib -Wl,-rpath,/opt/intel/oneapi/compiler/2022.2.1/mac/compiler/lib -L/opt/intel/oneapi/tbb/2021.7.1/lib -L/opt/intel/oneapi/ippcp/2021.6.2/lib -L/opt/intel/oneapi/ipp/2021.6.2/lib -L/opt/intel/oneapi/dnnl/2022.2.1/cpu_iomp/lib -L/opt/intel/oneapi/dal/2021.7.1/lib -L/opt/intel/oneapi/compiler/2022.2.1/mac/compiler/lib -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -Wl,-rpath,/opt/intel/oneapi/compiler/2022.2.1/mac/bin/intel64/../../compiler/lib -L/opt/intel/oneapi/compiler/2022.2.1/mac/bin/intel64/../../compiler/lib -Wl,-rpath,/Library/Developer/CommandLineTools/usr/lib/clang/14.0.3/lib/darwin -L/Library/Developer/CommandLineTools/usr/lib/clang/14.0.3/lib/darwin -lpetsc -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -lX11 -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lopen-rte -lopen-pal -limf -lm -lz -lifport -lifcoremt -lsvml -lipgo -lirc -lpthread -lclang_rt.osx -lmpi -lopen-rte -lopen-pal -limf -lm -lz -lsvml -lirng -lc++ -lipgo -ldecimal -lirc -lclang_rt.osx -lmpi -lopen-rte -lopen-pal -limf -lm -lz -lsvml -lirng -lc++ -lipgo -ldecimal -lirc -lclang_rt.osx -o ex19
icc: remark #10441: The Intel(R) C++ Compiler Classic (ICC) is deprecated and will be removed from product release in the second half of 2023. The Intel(R) oneAPI DPC++/C++ Compiler (ICX) is the recommended compiler moving forward. Please transition to use this compiler. Use '-diag-disable=10441' to disable this message.
In file included from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscsys.h(44),
                 from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscvec.h(9),
                 from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscmat.h(7),
                 from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscpc.h(7),
                 from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscksp.h(7),
                 from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscsnes.h(7),
                 from ex19.c(68):
/Users/mnv/Documents/Software/petsc-3.19.1/include/petscsystypes.h(68): warning #2621: attribute "warn_unused_result" does not apply here
  PETSC_ERROR_CODE_TYPEDEF enum PETSC_ERROR_CODE_NODISCARD {
                                ^

Possible error running C/C++ src/snes/tutorials/ex19 with 1 MPI process
[excess:37807] *** Process received signal ***
[excess:37807] Signal: Segmentation fault: 11 (11)
[excess:37807] Signal code: Address not mapped (1)
[excess:37807] Failing at address: 0x7f
[excess:37807] *** End of error message ***
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec noticed that process rank 0 with PID 0 on node excess exited on signal 11 (Segmentation fault: 11).
--------------------------------------------------------------------------
Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes
[excess:37831] *** Process received signal ***
[excess:37831] Signal: Segmentation fault: 11 (11)
[excess:37831] Signal code: Address not mapped (1)
[excess:37831] Failing at address: 0x7f
[excess:37831] *** End of error message ***
[excess:37832] *** Process received signal ***
[excess:37832] Signal: Segmentation fault: 11 (11)
[excess:37832] Signal code: Address not mapped (1)
[excess:37832] Failing at address: 0x7f
[excess:37832] *** End of error message ***
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec noticed that process rank 1 with PID 0 on node excess exited on signal 11 (Segmentation fault: 11).
--------------------------------------------------------------------------
Possible error running Fortran example src/snes/tutorials/ex5f with 1 MPI process
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image              PC                Routine            Line        Source            
libifcoremt.dylib  000000010B7F7FE4  for__signal_handl     Unknown  Unknown
libsystem_platfor  00007FF8024C25ED  _sigtramp             Unknown  Unknown
ex5f               00000001087AFA38  PetscGetArchType      Unknown  Unknown
ex5f               000000010887913B  PetscErrorPrintfI     Unknown  Unknown
ex5f               000000010878D227  PetscInitialize_C     Unknown  Unknown
ex5f               000000010879D289  petscinitializef_     Unknown  Unknown
ex5f               0000000108713C09  petscsys_mp_petsc     Unknown  Unknown
ex5f               0000000108710B5D  MAIN__                Unknown  Unknown
ex5f               0000000108710AEE  main                  Unknown  Unknown
dyld               00007FF80213B41F  start                 Unknown  Unknown
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[48108,1],0]
  Exit code:    174
--------------------------------------------------------------------------
Completed test examples
Error while running make check
make[1]: *** [check] Error 1
make: *** [check] Error 2

From: Vanella, Marcos (Fed) <marcos.vanella@nist.gov>
Sent: Monday, May 15, 2023 12:20 PM
To: Matthew Knepley <knepley@gmail.com>
Cc: petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov>
Subject: Re: [petsc-users] Compiling PETSC with Intel OneAPI compilers and OpenMPI
 
Thank you Matt I'll try this and let you know.
Marcos
From: Matthew Knepley <knepley@gmail.com>
Sent: Monday, May 15, 2023 12:08 PM
To: Vanella, Marcos (Fed) <marcos.vanella@nist.gov>
Cc: petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov>
Subject: Re: [petsc-users] Compiling PETSC with Intel OneAPI compilers and OpenMPI
 
On Mon, May 15, 2023 at 11:19 AM Vanella, Marcos (Fed) via petsc-users <petsc-users@mcs.anl.gov> wrote:
Hello, I'm trying to compile the PETSc library version 3.19.1 with OpenMPI 4.1.4 and the OneAPI 2022 Update 2 Intel Compiler suite on a Mac with OSX Ventura 13.3.1.
I can compile PETSc in debug mode with this configure and make lines. I can run the PETSC tests, which seem fine.
When I compile the library in optimized mode, either using -O3 or O1, for example configuring with:

I hate to yell "compiler bug" when this happens, but it sure seems like one. Can you just use

  --with-debugging=0

without the custom COPTFLAGS, CXXOPTFLAGS, FOPTFLAGS? If that works, it is almost
certainly a compiler bug. If not, then we can go in the debugger and see what is failing.

  Thanks,

    Matt
 
$ ./configure --prefix=/opt/petsc-oneapi22u3 --with-blaslapack-dir=/opt/intel/oneapi/mkl/2022.2.1 COPTFLAGS='-m64 -O1 -g -diag-disable=10441' CXXOPTFLAGS='-m64 -O1 -g -diag-disable=10441' FOPTFLAGS='-m64 -O1 -g' LDFLAGS='-m64' --with-debugging=0 --with-shared-libraries=0 --download-make

and using mpicc (icc), mpif90 (ifort) from  Open MPI, the static lib compiles. Yet, I see right off the bat this segfault error in the first PETSc example:

$ make PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 PETSC_ARCH=arch-darwin-c-opt test
/Users/mnv/Documents/Software/petsc-3.19.1/arch-darwin-c-opt/bin/make --no-print-directory -f /Users/mnv/Documents/Software/petsc-3.19.1/gmakefile.test PETSC_ARCH=arch-darwin-c-opt PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1 test
/opt/intel/oneapi/intelpython/latest/bin/python3 /Users/mnv/Documents/Software/petsc-3.19.1/config/gmakegentest.py --petsc-dir=/Users/mnv/Documents/Software/petsc-3.19.1 --petsc-arch=arch-darwin-c-opt --testdir=./arch-darwin-c-opt/tests
Using MAKEFLAGS: --no-print-directory -- PETSC_ARCH=arch-darwin-c-opt PETSC_DIR=/Users/mnv/Documents/Software/petsc-3.19.1
         CC arch-darwin-c-opt/tests/sys/classes/draw/tests/ex1.o
In file included from /Users/mnv/Documents/Software/petsc-3.19.1/include/petscsys.h(44),
                 from /Users/mnv/Documents/Software/petsc-3.19.1/src/sys/classes/draw/tests/ex1.c(4):
/Users/mnv/Documents/Software/petsc-3.19.1/include/petscsystypes.h(68): warning #2621: attribute "warn_unused_result" does not apply here
  PETSC_ERROR_CODE_TYPEDEF enum PETSC_ERROR_CODE_NODISCARD {
                                ^

    CLINKER arch-darwin-c-opt/tests/sys/classes/draw/tests/ex1
       TEST arch-darwin-c-opt/tests/counts/sys_classes_draw_tests-ex1_1.counts
not ok sys_classes_draw_tests-ex1_1 # Error code: 139
#     [excess:98681] *** Process received signal ***
#     [excess:98681] Signal: Segmentation fault: 11 (11)
#     [excess:98681] Signal code: Address not mapped (1)
#     [excess:98681] Failing at address: 0x7f
#     [excess:98681] *** End of error message ***
#     --------------------------------------------------------------------------
#     Primary job  terminated normally, but 1 process returned
#     a non-zero exit code. Per user-direction, the job has been aborted.
#     --------------------------------------------------------------------------
#     --------------------------------------------------------------------------
#     mpiexec noticed that process rank 0 with PID 0 on node excess exited on signal 11 (Segmentation fault: 11).
#     --------------------------------------------------------------------------
 ok sys_classes_draw_tests-ex1_1 # SKIP Command failed so no diff

I see the same segfault error in all PETSc examples. 
Any help is mostly appreciated, I'm starting to work with PETSc. Our plan is to use the linear solver from PETSc for the Poisson equation on our numerical scheme and test this on a GPU cluster. So also, any guideline on how to interface PETSc with a fortran code and personal experience is also most appreciated!

Marcos





-- 
What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener



-- 
What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.
-- Norbert Wiener